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Crystal structure of 1-(beta-D-glucopyranosyl)-4-substituted-1,2,3-triazoles in complex with glycogen phosphorylase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PRJ PDB entry 2PRJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 SMALL TUBES 6.8 289 pH 6.8, SMALL TUBES, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.4 48.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.287 α = 90 b = 127.287 β = 90 c = 115.615 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARRESEARCH 2008-12-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.80100 EMBL/DESY, HAMBURG X13
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.03 30 96.7 0.063 11.5 5.9 60007 32.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.03 2.06 98.3 0.551 4.3 5.8 2991
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2PRJ 2.03 29.83 56675 3049 96.72 0.19697 0.19572 0.1954 0.22019 RANDOM 37.272
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.771 r_dihedral_angle_4_deg 17.614 r_dihedral_angle_3_deg 15.277 r_dihedral_angle_1_deg 5.218 r_scangle_it 2.084 r_scbond_it 1.272 r_angle_refined_deg 1.035 r_mcangle_it 0.949 r_mcbond_it 0.541 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.771 r_dihedral_angle_4_deg 17.614 r_dihedral_angle_3_deg 15.277 r_dihedral_angle_1_deg 5.218 r_scangle_it 2.084 r_scbond_it 1.272 r_angle_refined_deg 1.035 r_mcangle_it 0.949 r_mcbond_it 0.541 r_nbtor_refined 0.307 r_nbd_refined 0.189 r_symmetry_vdw_refined 0.151 r_symmetry_hbond_refined 0.127 r_xyhbond_nbd_refined 0.113 r_chiral_restr 0.073 r_bond_refined_d 0.006 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6576 Nucleic Acid Atoms Solvent Atoms 216 Heterogen Atoms 49
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling